What Once Was Lost
by Andie O'Neill
Summary: They’d finally found Elizabeth after being missing for a year, but when Elizabeth refuses to return to Atlantis, Sheppard may just have to lose her all over again.


What Once Was Lost

By Andie O'Neill

Summary: They'd finally found Elizabeth after being missing for a year, but when Elizabeth refuses to return to Atlantis, Sheppard may just have to lose her all over again.

A/N: Spoilers for Lifeline! I might make a few more one shots of this… make it into a series or something… we'll see. Just tell me if ya like it and I'll think about it! ;)

When Lorne walked through the gate he was unable to suppress the worry on his face as he looked back at the shimmering puddle, watching it shut down. Their radios had been damaged beyond repair, leaving him one option, return to Atlantis and explain the situation.

"Major Lorne? Where's your team?" Colonel Carter asked as she walked down the steps to meet him, worried.

"Their fine, everyone's okay," he assured her. "I need to speak with you, Colonel… we have a situation."

"What kind of situation?" she asked confused.

Lorne took in a deep breath. "I'd rather discuss this in private… I think Sheppard and his team will want to hear this too. My team and I… kinda ran into some trouble."

"Trouble?" she questioned, suddenly back to worried.

"Replicators."

Carter frowned at that, and turned on her radio. "Colonel Sheppard, I need you to collect your team immediately and meet me in the briefing room."

John wasn't really sure why he and his team were called, but he could hear the worry in Carter's voice. Something was wrong. Sheppard and Ronan exchanged a brief look before focusing on Lorne who looked fairly shaken up. "So what happened?" he finally asked.

Lorne looked down, a far away look in his eyes. "They were looking for someone. There was a village there, but most had been slaughtered. Only a few survived… including someone we never thought we'd see again. Doctor Weir was with them."

"What?" exclaimed Rodney.

"She's alive?" John asked quietly.

Lorne shook his head. "We tried to ask her a few questions, but she was a little out of it. The villagers were happy to explain… apparently she destroyed the Replicators that had attacked the planet. They just started falling apart… ships fell from the sky. During the attack she'd been injured but was able to use the energy she had to somehow link with the Replicators."

John nodded. "That's how she helped us. She froze them so we could escape."

"No sir, this is different. The survivors were with her when the Replicators were destroyed. She just closed her eyes, sir. Then when she opened them she told the villagers they were gone. There was Replicator ships… all destroyed. By the time we came… more had already gone through the gate. Doctor Weir saved our life… we just thought something had happened to make them fall apart… but it was her. She stopped them."

Rodney was already ready to solve the mystery. "It could be that she's become powerful enough to actually link with them without physical contact."

"We didn't want to bring her in without talking to you first."

Sam nodded. "We need to know how she destroyed those Replicators. If she's that powerful, she may be the only thing that could stop them once they completely destroy the Wraith."

Lorne nodded.

"I'd like to go with him, Colonel. Elizabeth and I were friends… I can help!" John added before the meeting would be over.

"And I'll need to be there for obvious reasons," said Rodney.

"I could help protect them in case anymore Replicators come and Doctor Weir doesn't have the strength."

"I would also like to help Ronan," Teyla told them.

Sam smiled. "Lorne, it looks like Sheppard's team is coming with you. Get ready, you leave just as soon as you're ready. Dismissed."

When Elizabeth awoke she smiled to see the man standing over her, applying a wet cloth to her forehead. "When did you get here?" she asked.

He smiled, stroking her cheek for just a moment, to anyone else it was barely a brush… to Elizabeth it said everything he'd could never actually say. "About an hour ago. You passed out. I guess you were pretty tired, although who wouldn't be after destroying a Replicator armada."

"It wasn't an armada," she corrected him.

"We took a puddlejumper. We saw the ships in orbit."

Elizabeth sighed. She should have known better. "There were only a few ships."

"We counted at least twelve."

It was almost a year later and he could still annoy her. "I may not be your boss anymore, but I can still order you to shut up."

John laughed at that. "Need anything? Hungry? Thirsty?"

Elizabeth swallowed; her mouth dry. "Water would be nice."

John nodded and turned around to grab some water he'd obviously known she'd need. He gently helped her drink.

"Thanks."

John frowned, putting the water down. "How did you destroy those Replicators, Elizabeth."

Elizabeth frowned, looking away.

"We need to know. If there's any chance it could help us destroy the Replicators-"

"No John! Just stop!"

"Elizabeth-"

"I'm not some experiment, John! And I will not go back to Atlantis!"

"Elizabeth-"

"No! You're not taking me back!" Elizabeth shouted, her face stricken with fear. John was shocked by the tears coming down her eyes. Elizabeth understood his confusion, but he had to understand. "The Replicators will stop at nothing to get me back, John. I'm not just the key to destroying the Replicators, I'm also the key to destroying Earth… and Atlantis. I will not go to Atlantis and I WILL NOT GO TO EARTH. I'd rather die."

"Why not? If the Replicators want you, we can hide you!"

"I killed those Replicators because I was still linked with them… all of them, John."

"If that's true they would be able to take control of you."

Elizabeth shook her head. "They can't. They've tried, but the more they tried the more I learned how to stop them. I was too powerful."

"How did you escape?" he asked her.

Elizabeth closed her eyes. "John-"

"Why won't you just tell me what's going on so I can help you, Elizabeth?!"

Elizabeth's energy was returning thanks to the nanities inside her. She got out of bed weakly, backing away from him. Unfortunately it had yet to return completely. She fell to the floor, wincing in pain.

"Elizabeth!" John ran to her, helping her back to bed. "You aren't strong enough yet."

Elizabeth watched him take her to the bed. Once she was back she sat up, shaking.

John was worried, she knew that much. He sat on the bed beside her, moving a hand behind her to help keep her up. "Look, I'm sorry if I upset you. It's just… Lorne saw what you did."

Elizabeth knew she had to tell him. "I had friends…."

John frowned confused. "Friends."

"When you left me in the Replicator city… they took me into one of their labs. The scientist there… he…" Elizabeth tried to get out. John wiped away the tears that came almost immediately.

"It's okay… just tell me. Did he hurt you?"

Elizabeth shook her head. "No… he was a good man. His name was Beck; at least that's what I called him. He liked it when I called him that. His full name was Beckore. Oberoth wanted him to study me… learn my weakness. One of the first things they did was inject nanities… they were to keep the link between myself and Beck open so he could study my mind. He reminded me a lot of Niam. He was fascinated with all I knew of ascension. We became friends."

John knew something big happened for her to be this upset. "He helped you escape?"

Elizabeth smiled. "Beck needed my help… so I gave it to him. I taught him everything I knew about the Ancients, and he taught me everything I could ever know about the Replicators. They wanted to use me to destroy Atlantis as well as Earth. Instead Beck found a way to use me to destroy the Replicators."

John almost smiled at that. He wasn't at all surprised that Elizabeth got him to help her. She was good at that. "You made a deal with him?"

Elizabeth shook her head. "Beck knew what the Replicators were up to. He chose me over his people, but I never asked him to. Truthfully I never wanted him to…."

_**FLASHBACK**_

"_Beck, do you have any idea what you'd be doing?! When they learned what Niam was up to they took control of him!"_

_Beck took a step to her, taking her hand in his to calm her down. "We will destroy you, Elizabeth. I will not let them destroy you or your people." He rested his forehead with hers and Elizabeth felt the surge of feelings, his feelings… for her. Suddenly his lips were on hers and she knew he'd already sealed his fate. "Goodbye Elizabeth."_

_**END OF FLASHBACK**_

"He sacrificed himself for you?" John asked, surprised.

Elizabeth fought her tears, but it was useless. "I killed him. Suddenly I had the power to destroy the Replicators… I didn't know how to use it and he knew it. I don't even know if he ascended. The whole city… I destroyed everyone with a single thought. Once I realized what I'd done I ran… I barely made it out. Beck's nanities allowed for a continuous link to the Replicators. In doing so I can destroy them."

"Then why haven't you?" John asked.

"I need to be nearby for the transmission to make it to them. When the Replicators attacked this planet I was hurt… unconscious. I could only stop them when one of the villagers woke me up. They know what I can do. They've been trying to kill me since I escaped. I've gone from planet to planet in the hopes of escaping them. I guess my time with Ronan taught me a thing or two about running."

John was at a loss. Was it possible? Was it possible the key to destroying the Replicators was right before him? He didn't know what to say. "Sounds like you've had a hard year," he almost whispered.

Elizabeth smiled through her tears, relived to have him beside her again. She'd missed Atlantis so much in the year she'd been away. "John, you have to understand why I can't go back with you. I can't go to Earth or Atlantis… not while I'm linked to them. They'd know your position and they'd attack just like before. I won't let that happen."

"Elizabeth, we could find a way to cut the link. I'm sure Rodney will figure it out!"

Elizabeth shook her head. "John, you know what an advantage this is. I have the power to destroy the Replicators-"

"Which is exactly why we need you back!" John cut in.

Elizabeth sighed. It'd been a long time, but it was obvious John hadn't changed much. He never left a man behind… except Ford… and her. It was almost ironic. Ford had gone crazy and refused to go back until everyone understood he wasn't crazy, and he felt he had a job to do… destroy the Wraith. She couldn't go back because she would put Atlantis in danger, but she too had a job to do… destroy the Replicators. She was almost starting to understand why Aiden Ford did what he did. "You don't have to protect me anymore, John. I can take care of myself. I've been gone a long time… I had to learn to protect myself, and the nanities heal my wounds. I'll give you the addresses I'm going to next in case you need me, and maybe you could give me a radio. I try not to stay more than a day."

"Elizabeth-"

Elizabeth stopped him from saying a word, kissing his lips gently and lovingly. When she finally broke the kiss to breathe she could see the ache in John's eyes. He didn't want to say goodbye. Neither did she. "One day I'll stop them… and come back with you."

John smiled at that, resting his forehead on hers. "Beck… he loved you didn't he."

Elizabeth frowned. She tried so hard to forget him, but they'd shared too much. A part of him would always remain in her. "Don't even try to tell me there weren't others. I know you better than that."

"None like you," he told her.

Elizabeth moved away, closing her eyes as Beck's face appeared in her mind. "I was only there for a few months… but we shared more than I have with any other person. We were connected."

Although saddened by what she said John couldn't help but think of the woman he'd shared himself with… Chaya. They'd shared something special, yet somehow he'd come to care about Elizabeth far more than he could have ever loved the Ancient woman. He wasn't really sure why. "I guess I can understand that."

"I used to tell him about you all the time. You would have liked him. Actually, you two probably would have gotten along, he was so much like you. He liked to make me laugh."

Although jealous, John understood the part 'Beck' had played in her life. "I guess we were a lot alike if he protected you, gave his life for you. I know I would."

Elizabeth kissed him once more. "I know you would, John. I know."

John pulled her in his arms and held her there for hours. She told him about her travels during the year they'd been apart, and he told her of all the adventures he and his team had shared. They knew tomorrow it would be over. She would have to leave before more Replicators came.

It had taken longer than Elizabeth would have liked to pack, but she was finally finished, her backpack zipped up and ready. She took in a deep breath before leaving the tent to see her friends before her. Teyla smiled and walked up to her first. Elizabeth immediately hugged the woman. "You take care. Tell Halling and Jinto I'm thinking about them."

"I will, Elizabeth. I shall miss you."

Elizabeth let go of her friend, smiling. "I'll miss you too."

When Teyla finally backed away Ronan was next to walk up to her. He too pulled her into a hug, stronger than Teyla's. Elizabeth laughed at the six foot bear before her. She never would have believed she'd miss the quiet man before her. "You have a warrior's spirit, never lose that," he whispered to her. "When you've finished what you have to do, we'll be here."

Elizabeth almost cried when she finally let go of the friend before her. "I won't forget, Ronan." Her experience only made their friendship stronger. When she'd finally woken up she'd talked to him over breakfast, telling him how hard it'd been… always worried she'd bring the Replicators if she stayed too long. "Thank you, Ronan… for everything."

Ronan nodded and moved away. Rodney rushed to her before John could, grabbing her into a hug. "Take care out there, Elizabeth!"

Elizabeth patted the scientist's back. "Don't worry, Rodney, I'll be fine."

Rodney wouldn't let go. Elizabeth dropped her arms and sighed.

"Alright, alright… would you get off her?!" John cut in, pulling Rodney away. Elizabeth tried not to show her gratitude… for McKay's say.

"I was just saying goodbye!" Rodney fought.

John rolled his eyes and walked up to Elizabeth. He smiled, but Elizabeth knew it was just a show. "You sure you're going to be okay?" he asked gently.

"I'll be fine, John. I promise," he assured him.

John nodded. "Don't call us, we'll call you," he joked, trying to lighten the mood.

Elizabeth didn't take the bait though. She knew what he was doing. "Goodbye John."

"We'll see each other again… I'm sure of it."

Elizabeth nodded, not quite so sure. Slowly she invaded his space and pulled him down for a kiss to everyone's surprise. John seemed surprise as well, but not for long. When they finally parted Elizabeth could see the fire in his eyes. Everything would be okay. "Keep in touch," she whispered before giving one last look at the people who'd become family to her. She was doing this for them… it was all for them. "Take care of my city," she told them all and turned away from them. She forced each step she took as she headed to the gate, ignoring the tear that rolled down her face. _Until next time, John…._

The End

A/N: I really only wrote this because I was having some trouble writing Atlantis after watching Lifeline, but I finally got an idea and this was the result! My mojo's back! Yay:D


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